Last updated on 2025-07-26 08:49:13 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 10.71 | 142.37 | 153.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 7.05 | 100.90 | 107.95 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 240.27 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 242.79 | OK | |||
| r-devel-windows-x86_64 | 1.1.0 | 15.00 | 156.00 | 171.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 12.30 | 134.17 | 146.47 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 9.38 | 133.50 | 142.88 | OK | |
| r-release-macos-arm64 | 1.1.0 | 96.00 | ERROR | |||
| r-release-macos-x86_64 | 1.1.0 | 118.00 | ERROR | |||
| r-release-windows-x86_64 | 1.1.0 | 14.00 | 158.00 | 172.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 78.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.1.0 | 105.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 18.00 | 210.00 | 228.00 | NOTE |
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:
> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ### matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
>
> ### ** Examples
>
> expression.matrix.preproc <- as.matrix(read.csv(
+ system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"),
+ row.names = 1
+ ))[1:100, 1:4]
>
> anno <- AnnotationDbi::select(
+ getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+ keys = rownames(expression.matrix.preproc),
+ keytype = 'ENSEMBL',
+ columns = 'SYMBOL'
+ ) %>%
+ dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+ dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘GEO_App.Rmd’ using rmarkdown
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178620&format=file&file=GSE178620%5Fraw%5Fabundances%2Ecsv%2Egz'
Content type 'text/html' length 13683 bytes (13 KB)
==================================================
downloaded 13 KB
Quitting from GEO_App.Rmd:59-67 [read]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `read.table()`:
! duplicate 'row.names' are not allowed
---
Backtrace:
▆
1. ├─base::as.matrix(read.csv(download_path, row.names = 1))
2. └─utils::read.csv(download_path, row.names = 1)
3. └─utils::read.table(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GEO_App.Rmd' failed with diagnostics:
duplicate 'row.names' are not allowed
--- failed re-building ‘GEO_App.Rmd’
--- re-building ‘IntegratingMultiomics.Rmd’ using rmarkdown
--- finished re-building ‘IntegratingMultiomics.Rmd’
--- re-building ‘bulkAnalyseR.Rmd’ using rmarkdown
--- finished re-building ‘bulkAnalyseR.Rmd’
SUMMARY: processing the following file failed:
‘GEO_App.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: installed package size
Result: NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 2.3Mb
extdata 3.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64